org.jscience.ml.cml.cmlimpl
Class BaseToolImpl

java.lang.Object
  org.jscience.ml.cml.cmlimpl.BaseToolImpl

All Implemented Interfaces:

BaseTool

public class BaseToolImpl
extends java.lang.Object
implements BaseTool

Performs editing functions on a generic CMLObject

Field Summary

protected AbstractBase	abstractBase
protected static java.util.Hashtable	baseToolTable
protected static java.lang.String	CONSTRUCT
protected boolean	debug
protected java.lang.reflect.Constructor[]	declaredPublicConstructors
protected java.lang.reflect.Method[]	declaredPublicMethods
protected AbstractCMLDocument	document
protected static java.lang.String	editorPackageName
protected java.util.Hashtable	ignoreAttributeTable
protected static JumboLogger	jumboLogger
protected static java.lang.String	TEST
protected Workflow	workflow

Fields inherited from interface org.jscience.ml.cml.BaseTool

DOUBLE, INTEGER, STRING, XSD_DOUBLE, XSD_INTEGER, XSD_STRING

Constructor Summary

protected	BaseToolImpl() new BaseTool.
protected	BaseToolImpl(AbstractBase base)
	BaseToolImpl(AbstractCMLDocument document) new BaseTool containing a new AbstractBase.

Method Summary

void	characters(SaxHandler saxHandler, java.lang.String content) SAX2 parsing routine - called from characters() callback NOT namespace aware
static void	clear(java.util.Hashtable editorTable) clears an editorTable.
protected void	constructorsUsage()
static java.lang.String	convertClassToInterface(java.lang.String className) converts CML classname to interface.
static java.lang.String	convertInterfaceToClass(java.lang.String interfaceName) converts CMLInterface to class.
void	copyAttributesFromTo(AbstractBase from, AbstractBase to) copy attributes from one AbstractBase to another.
static BaseTool	createToolForName(java.lang.String baseName) constructs a tools class object.
protected void	debug(java.lang.String s) output string if debug set
void	endElement(SaxHandler saxHandler) SAX2 parsing routine - called from endElement() callback NOT namespace aware
boolean	equals(BaseTool baseTool) is the contained object equal to the other contained object.
java.lang.String	formatNumber(java.lang.String s)
AbstractBase	getAbstractBase() get abstract base only defined for implemented editors (default => null)
AbstractCMLDocument	getCMLDocument()
protected java.lang.reflect.Constructor	getConstructor(java.util.List argVector)
boolean	getDebug() debug status
java.lang.reflect.Constructor[]	getDeclaredPublicConstructors() get all public constructors belonging just to this class.
java.lang.reflect.Method[]	getDeclaredPublicMethods() get all public methods belonging just to this class.
protected static double[]	getDoubleArgs(int start, int nargs, java.lang.String[] args)
protected java.lang.reflect.Method	getMethod(java.lang.String methodS, java.util.List argVector)
BaseTool	getTestInstance(AbstractCMLDocument doc, int serial) a standard instance for testing.
static BaseTool	getTool(AbstractBase base) gets tool or creates new one.
static BaseTool	getTool(AbstractBase base, BaseTool tool) gets existing tool for base or returns tool after initialising it with base.
protected java.lang.reflect.Method	getUniqueMethod(java.lang.String methodS) gets unique method if possible does not use args at present
Workflow	getWorkflow() get the workflow.
protected void	methodsUsage()
void	mustEqual(BaseTool otherTool) throws exception if the contained object is not equal to the other contained object.
void	mustEqualAttributes(BaseTool otherTool)
void	mustEqualChildNodes(BaseTool otherTool)
void	processArgs(java.lang.String[] args) process args.
int	processCommandLine(java.lang.String[] args, int offset, java.util.List argVector, AbstractCMLDocument doc) process the commandline from main routines.
void	processCurrentCommand(Workflow workflow) run workflow script or object.
org.w3c.dom.Element	removeElement(java.lang.String elementName) removes the first element by tagName finds first element with that name and removes it from its parent.
java.lang.Object	runConstructor(java.util.List argVector) run any public constructor introspects the above constructors Example: CMLVector3 projectOnto(CMLVector3 v) is called with v as arg v1, v2 and floatArg as dontCare and returns Object of type CMLVector3
java.lang.Object	runMethod(java.lang.String methodS, java.util.List argVector) run any public method introspects the above methods Example: CMLVector3 projectOnto(CMLVector3 v) is called with v as arg v1, v2 and floatArg as dontCare and returns Object of type CMLVector3 Returns without action if duplicate method name
void	setAbstractBase(AbstractBase ab) set abstract base only defined for implemented editors (default => null) should not be required in user code
void	setDebug(boolean d) toggle debugging
void	setIgnoreAttribute(java.lang.String name, boolean descend) ignore an attribute
static void	setToolPackage(java.lang.String pName) set Tool package.
void	startElement(SaxHandler saxHandler, org.xml.sax.Attributes attributes) SAX2 parsing routine - called from startElement() callback NOT namespace aware
protected void	superInit(AbstractBase base)
void	testMethods() test all declared public methods.
void	transferChildrenFromTo(AbstractBase from, AbstractBase to) transfer children from one AbstractBase to another.
protected void	usage(java.lang.String className)
void	writeXML(java.io.Writer w, java.lang.String control) write XML, using class-specific information NOT namespace aware

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

jumboLogger

protected static JumboLogger jumboLogger

editorPackageName

protected static java.lang.String editorPackageName

CONSTRUCT

protected static java.lang.String CONSTRUCT

TEST

protected static java.lang.String TEST

baseToolTable

protected static java.util.Hashtable baseToolTable

abstractBase

protected AbstractBase abstractBase

document

protected AbstractCMLDocument document

debug

protected boolean debug

ignoreAttributeTable

protected java.util.Hashtable ignoreAttributeTable

workflow

protected Workflow workflow

declaredPublicMethods

protected java.lang.reflect.Method[] declaredPublicMethods

declaredPublicConstructors

protected java.lang.reflect.Constructor[] declaredPublicConstructors

Constructor Detail

BaseToolImpl

protected BaseToolImpl()

new BaseTool.

only for use by subclasses

BaseToolImpl

public BaseToolImpl(AbstractCMLDocument document)

new BaseTool containing a new AbstractBase.

uses document as owner

Parameters:

document - the owner document

BaseToolImpl

protected BaseToolImpl(AbstractBase base)

Method Detail

superInit

protected void superInit(AbstractBase base)

getTool

public static BaseTool getTool(AbstractBase base)

gets tool or creates new one.

Parameters:

base -

Returns:

the tool (null if molecule is null)

getTool

public static BaseTool getTool(AbstractBase base,
                               BaseTool tool)

gets existing tool for base or returns tool after initialising it with base.

Parameters:

base - the item that you want a tool for

tool - the tool to use should base not already have one

Returns:

the tool (null if molecule is null)

getCMLDocument

public AbstractCMLDocument getCMLDocument()

getAbstractBase

public AbstractBase getAbstractBase()

get abstract base

only defined for implemented editors (default => null)

Specified by:

getAbstractBase in interface BaseTool

Returns:

the element associated with this editor (null for default)

setAbstractBase

public void setAbstractBase(AbstractBase ab)

set abstract base

only defined for implemented editors (default => null) should not be required in user code

Specified by:

setAbstractBase in interface BaseTool

Parameters:

ab - the element associated with this editor

equals

public boolean equals(BaseTool baseTool)

is the contained object equal to the other contained object.

The two objects contained in the elements are compared. The default is to use an element-by-element and attribute-by-attribute comparison. This can be overridden for subclasses. For example the order of children in some elements matters while in others (e.g. molecules) it does not. The compared object must be of the same class but may have different namespace prefix, etc. By default ownerDocuments are ignored (thus molecules in different documents can be compared.)

childElements are compared using their equals() methods

The editors may have special methods to affect of control equality. Thus it is possible to ignore Ids.

If the reason for non-equality is required, the mustEqual() method should be used.

Specified by:

equals in interface BaseTool

Parameters:

baseTool - the other element editor (must be of same class)

mustEqual

public void mustEqual(BaseTool otherTool)
               throws CMLException

throws exception if the contained object is not equal to the other contained object.

see equals() for strategy.

Specified by:

mustEqual in interface BaseTool

Parameters:

otherTool - the other element (must be of same class)

Throws:

CMLException - the reason for non-equality

mustEqualAttributes

public void mustEqualAttributes(BaseTool otherTool)
                         throws CMLException

Throws:

CMLException

mustEqualChildNodes

public void mustEqualChildNodes(BaseTool otherTool)
                         throws CMLException

Throws:

CMLException

setIgnoreAttribute

public void setIgnoreAttribute(java.lang.String name,
                               boolean descend)

ignore an attribute

Specified by:

setIgnoreAttribute in interface BaseTool

Parameters:

name - attribute to ignore

descend - carry over to descendants

removeElement

public org.w3c.dom.Element removeElement(java.lang.String elementName)

removes the first element by tagName

finds first element with that name and removes it from its parent. mainly for debugging

Specified by:

removeElement in interface BaseTool

Returns:

the element removed

characters

public void characters(SaxHandler saxHandler,
                       java.lang.String content)
                throws CMLException

SAX2 parsing routine - called from characters() callback

NOT namespace aware

Specified by:

characters in interface BaseTool

Parameters:

saxHandler - SaxHandler

content - throws exception (probably application specific)

Throws:

CMLException

endElement

public void endElement(SaxHandler saxHandler)
                throws CMLException

SAX2 parsing routine - called from endElement() callback

NOT namespace aware

Specified by:

endElement in interface BaseTool

Parameters:

saxHandler - Saxhandler throws exception (probably application specific)

Throws:

CMLException

startElement

public void startElement(SaxHandler saxHandler,
                         org.xml.sax.Attributes attributes)
                  throws CMLException

SAX2 parsing routine - called from startElement() callback

NOT namespace aware

Specified by:

startElement in interface BaseTool

Parameters:

saxHandler - Saxhandler

attributes - the attribute list throws exception (probably application specific)

Throws:

CMLException

writeXML

public void writeXML(java.io.Writer w,
                     java.lang.String control)
              throws CMLException,
                     java.io.IOException

write XML, using class-specific information

NOT namespace aware

Specified by:

writeXML in interface BaseTool

Parameters:

w - the writer

control - (concatenation of CML version and array)

Throws:

exception - (probably application specific)

CMLException

java.io.IOException

setDebug

public void setDebug(boolean d)

toggle debugging

Parameters:

d - debug

getDebug

public boolean getDebug()

debug status

Returns:

is debug set

debug

protected void debug(java.lang.String s)

output string if debug set

Parameters:

s - string to output

copyAttributesFromTo

public void copyAttributesFromTo(AbstractBase from,
                                 AbstractBase to)

copy attributes from one AbstractBase to another.

overwrites existing atts

Specified by:

copyAttributesFromTo in interface BaseTool

Parameters:

from - element to copy from

to - element to copy to

transferChildrenFromTo

public void transferChildrenFromTo(AbstractBase from,
                                   AbstractBase to)

transfer children from one AbstractBase to another.

Specified by:

transferChildrenFromTo in interface BaseTool

Parameters:

from - element to copy from

to - element to copy to

clear

public static void clear(java.util.Hashtable editorTable)

clears an editorTable.

Parameters:

editorTable - the table to clear

setToolPackage

public static void setToolPackage(java.lang.String pName)

set Tool package.

Parameters:

pName - the package in which Tools will be found

createToolForName

public static BaseTool createToolForName(java.lang.String baseName)

constructs a tools class object.

at present converts "moleculeTool" to [currentPackage].MoleculeToolImpl Does NOT use or create a DOM, so only use for accesing class methods e.g. in workflow

Returns:

object (or null if cannot create)

processCurrentCommand

public void processCurrentCommand(Workflow workflow)
                           throws CMLException

run workflow script or object.

sets workflow to the tool and runs the current command all information (current command, symbolTables can be accessed from workflow

Specified by:

processCurrentCommand in interface BaseTool

Parameters:

workflow - to process.

Throws:

CMLException

getWorkflow

public Workflow getWorkflow()

get the workflow.

Specified by:

getWorkflow in interface BaseTool

Returns:

workflow

formatNumber

public java.lang.String formatNumber(java.lang.String s)

getDeclaredPublicConstructors

public java.lang.reflect.Constructor[] getDeclaredPublicConstructors()

get all public constructors belonging just to this class.

Returns:

array of constructors

getDeclaredPublicMethods

public java.lang.reflect.Method[] getDeclaredPublicMethods()

get all public methods belonging just to this class.

Specified by:

getDeclaredPublicMethods in interface BaseTool

Returns:

array of methods

runConstructor

public java.lang.Object runConstructor(java.util.List argVector)

run any public constructor introspects the above constructors Example: CMLVector3 projectOnto(CMLVector3 v) is called with v as arg v1, v2 and floatArg as dontCare and returns Object of type CMLVector3

Parameters:

argVector - arguments in order.

Returns:

the constructor value

runMethod

public java.lang.Object runMethod(java.lang.String methodS,
                                  java.util.List argVector)

run any public method introspects the above methods Example: CMLVector3 projectOnto(CMLVector3 v) is called with v as arg v1, v2 and floatArg as dontCare and returns Object of type CMLVector3 Returns without action if duplicate method name

Specified by:

runMethod in interface BaseTool

Parameters:

methodS - case-sensitive method.

argVector - arguments in order. First arg is instance of this

Returns:

any return value (see Method.invoke for classes)

getMethod

protected java.lang.reflect.Method getMethod(java.lang.String methodS,
                                             java.util.List argVector)

getConstructor

protected java.lang.reflect.Constructor getConstructor(java.util.List argVector)

getUniqueMethod

protected java.lang.reflect.Method getUniqueMethod(java.lang.String methodS)

gets unique method if possible does not use args at present

Parameters:

methodS - method name

Returns:

unique method for that name

getDoubleArgs

protected static double[] getDoubleArgs(int start,
                                        int nargs,
                                        java.lang.String[] args)

usage

protected void usage(java.lang.String className)

constructorsUsage

protected void constructorsUsage()

methodsUsage

protected void methodsUsage()

testMethods

public void testMethods()

test all declared public methods. introspects args and creates test instances from primitives or getTestInstance(); cannot create arg which require arrays so skips method also may skip some superclasses

convertInterfaceToClass

public static java.lang.String convertInterfaceToClass(java.lang.String interfaceName)

converts CMLInterface to class. e.g. converts org.jscience.ml.cml.CMLVector3 to org.jscience.ml.cml.cmlimpl.Vector3Impl and AbstractBase to CMLBaseImpl

Parameters:

interfaceName - the interface

Returns:

the class name

convertClassToInterface

public static java.lang.String convertClassToInterface(java.lang.String className)

converts CML classname to interface. e.g. converts org.jscience.ml.cml.cmlimpl.Vector3Impl to org.jscience.ml.cml.CMLVector3 and CMLBaseImpl to AbstractBase

Parameters:

className -

Returns:

the interface name

processArgs

public void processArgs(java.lang.String[] args)

process args.

Parameters:

args -

getTestInstance

public BaseTool getTestInstance(AbstractCMLDocument doc,
                                int serial)

a standard instance for testing. returns null unless subclassed

Specified by:

getTestInstance in interface BaseTool

Parameters:

doc - the owner document

serial - the instance (1,2,3)

Returns:

null

processCommandLine

public int processCommandLine(java.lang.String[] args,
                              int offset,
                              java.util.List argVector,
                              AbstractCMLDocument doc)

process the commandline from main routines. normally subclassed

Specified by:

processCommandLine in interface BaseTool

Parameters:

args - the arguments

offset - current position in args

argVector - vector to accumulate arguments

doc - owner document

Returns:

position in args after parsing